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Series GSE29781 Query DataSets for GSE29781
Status Public on Jan 20, 2012
Title Expression data from 30do mouse spermatid [Affymetrix]
Organism Mus musculus
Experiment type Expression profiling by array
Summary Chromatin performs numerous functions during cellular differentiation, and therefore it must be capable of adopting a multitude of different structures. How these various structures are established is poorly understood, but we propose that specific histone H2A variants will have a key role in remodelling chromatin during differentiation. Structurally, we show here that the gain of just a single acidic amino acid residue has generated a new mouse ‘H2A.Bbd-like’ histone variant, H2A.Lap1, and that when incorporated into nucleosomal arrays imparts on them unique biophysical properties that are distinct from arrays containing either H2A or human H2A.Bbd. Functionally, we identify H2A.Lap1 as a novel chromatin component of active genes that are expressed during spermatogenesis, and in combination with H2A.Z create a unique chromatin landscape at the start site of transcription. During round spermatid differentiation, H2A.Lap1 dramatically loads onto the inactive X chromosome enabling a subset of its genes to be transcriptionally activated.
We used microarrays together with ChIP-seq data in order to see distribution of Lap1 and expression level of the Lap1 associated genes
Overall design Total RNA was isolated using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen). Samples were DNase I treated (Roche) and reverse transcribed using Superscript II reverse transcriptase following the manufacturer’s recommendations (Invitrogen). DNA was either analysed by semi–quantitative PCR, real-time qPCR using SYBR Green PCR master mix (Applied Biosystems), or subjected to DNA microarray analysis (in triplicate) using the GeneChip Mouse Gene 1.0 ST Array (Affymetrix). Robust Multichip Average (RMA) correction and probe set summaries were obtained using Affymetrix Power Tools software annotation (Affymetrix) based on the mm9 mouse genome. Unless otherwise stated, all subsequent expression analyses (see Supplementary Methods) were performed in the R statistical computing environment (version 2.11.1).
Contributor(s) Soboleva T, Williams R
Citation(s) 22139013
Submission date Jun 07, 2011
Last update date Mar 04, 2019
Contact name Rohan Williams
Organization name ANU
Street address Garran Rd ACTON
City Canberra
State/province ACT
ZIP/Postal code 2601
Country Australia
Platforms (1)
GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
Samples (3)
GSM738186 30do mouse spermatids replicate 1
GSM738187 30do mouse spermatids replicate 2
GSM738188 30do mouse spermatids replicate 3
This SubSeries is part of SuperSeries:
GSE29916 Functional studies of a H2A.Bbd-like histone variant in mouse spermatogenesis
BioProject PRJNA155209

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE29781_RAW.tar 12.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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